workbench 0.8.197__py3-none-any.whl → 0.8.198__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
@@ -68,7 +68,7 @@ class Proximity:
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  self,
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  top_percent: float = 1.0,
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  min_delta: Optional[float] = None,
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- k_neighbors: int = 5,
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+ k_neighbors: int = 4,
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  ) -> pd.DataFrame:
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  """
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  Find compounds with steep target gradients (data quality issues and activity cliffs).
@@ -80,7 +80,7 @@ class Proximity:
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  Args:
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  top_percent: Percentage of compounds with steepest gradients to return (e.g., 1.0 = top 1%)
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  min_delta: Minimum absolute target difference to consider. If None, defaults to target_range/100
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- k_neighbors: Number of neighbors to use for median calculation (default: 5)
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+ k_neighbors: Number of neighbors to use for median calculation (default: 4)
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  Returns:
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  DataFrame of compounds with steepest gradients, sorted by gradient (descending)
@@ -113,23 +113,23 @@ class Proximity:
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  # Get k nearest neighbors (excluding self)
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  nbrs = self.neighbors(cmpd_id, n_neighbors=k_neighbors, include_self=False)
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- # Calculate median target of k nearest neighbors
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- neighbor_median = nbrs.head(k_neighbors)[self.target].median()
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+ # Calculate median target of k neighbors, excluding the nearest neighbor (index 0)
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+ neighbor_median = nbrs.iloc[1:k_neighbors][self.target].median()
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  median_diff = abs(cmpd_target - neighbor_median)
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  # Only keep if compound differs from neighborhood median
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  # This filters out cases where the nearest neighbor is the outlier
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  if median_diff >= min_delta:
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- mean_distance = nbrs.head(k_neighbors)["distance"].mean()
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-
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  results.append(
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  {
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  self.id_column: cmpd_id,
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  self.target: cmpd_target,
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+ "nn_target": row["nn_target"],
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+ "nn_target_diff": row["nn_target_diff"],
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+ "nn_distance": row["nn_distance"],
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+ "gradient": row["gradient"], # Keep Phase 1 gradient
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  "neighbor_median": neighbor_median,
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  "neighbor_median_diff": median_diff,
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- "mean_distance": mean_distance,
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- "gradient": median_diff / (mean_distance + epsilon),
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  }
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  )
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@@ -68,7 +68,7 @@ class Proximity:
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  self,
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  top_percent: float = 1.0,
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  min_delta: Optional[float] = None,
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- k_neighbors: int = 5,
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+ k_neighbors: int = 4,
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  ) -> pd.DataFrame:
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  """
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  Find compounds with steep target gradients (data quality issues and activity cliffs).
@@ -80,7 +80,7 @@ class Proximity:
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  Args:
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  top_percent: Percentage of compounds with steepest gradients to return (e.g., 1.0 = top 1%)
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  min_delta: Minimum absolute target difference to consider. If None, defaults to target_range/100
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- k_neighbors: Number of neighbors to use for median calculation (default: 5)
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+ k_neighbors: Number of neighbors to use for median calculation (default: 4)
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  Returns:
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  DataFrame of compounds with steepest gradients, sorted by gradient (descending)
@@ -113,23 +113,23 @@ class Proximity:
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  # Get k nearest neighbors (excluding self)
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  nbrs = self.neighbors(cmpd_id, n_neighbors=k_neighbors, include_self=False)
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- # Calculate median target of k nearest neighbors
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- neighbor_median = nbrs.head(k_neighbors)[self.target].median()
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+ # Calculate median target of k neighbors, excluding the nearest neighbor (index 0)
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+ neighbor_median = nbrs.iloc[1:k_neighbors][self.target].median()
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  median_diff = abs(cmpd_target - neighbor_median)
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  # Only keep if compound differs from neighborhood median
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  # This filters out cases where the nearest neighbor is the outlier
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  if median_diff >= min_delta:
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- mean_distance = nbrs.head(k_neighbors)["distance"].mean()
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-
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  results.append(
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  {
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  self.id_column: cmpd_id,
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  self.target: cmpd_target,
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+ "nn_target": row["nn_target"],
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+ "nn_target_diff": row["nn_target_diff"],
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+ "nn_distance": row["nn_distance"],
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+ "gradient": row["gradient"], # Keep Phase 1 gradient
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  "neighbor_median": neighbor_median,
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  "neighbor_median_diff": median_diff,
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- "mean_distance": mean_distance,
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- "gradient": median_diff / (mean_distance + epsilon),
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  }
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  )
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@@ -68,7 +68,7 @@ class Proximity:
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  self,
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  top_percent: float = 1.0,
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  min_delta: Optional[float] = None,
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- k_neighbors: int = 5,
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+ k_neighbors: int = 4,
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  ) -> pd.DataFrame:
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  """
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  Find compounds with steep target gradients (data quality issues and activity cliffs).
@@ -80,7 +80,7 @@ class Proximity:
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  Args:
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  top_percent: Percentage of compounds with steepest gradients to return (e.g., 1.0 = top 1%)
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  min_delta: Minimum absolute target difference to consider. If None, defaults to target_range/100
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- k_neighbors: Number of neighbors to use for median calculation (default: 5)
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+ k_neighbors: Number of neighbors to use for median calculation (default: 4)
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  Returns:
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  DataFrame of compounds with steepest gradients, sorted by gradient (descending)
@@ -113,23 +113,23 @@ class Proximity:
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  # Get k nearest neighbors (excluding self)
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  nbrs = self.neighbors(cmpd_id, n_neighbors=k_neighbors, include_self=False)
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- # Calculate median target of k nearest neighbors
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- neighbor_median = nbrs.head(k_neighbors)[self.target].median()
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+ # Calculate median target of k neighbors, excluding the nearest neighbor (index 0)
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+ neighbor_median = nbrs.iloc[1:k_neighbors][self.target].median()
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  median_diff = abs(cmpd_target - neighbor_median)
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  # Only keep if compound differs from neighborhood median
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  # This filters out cases where the nearest neighbor is the outlier
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  if median_diff >= min_delta:
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- mean_distance = nbrs.head(k_neighbors)["distance"].mean()
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-
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  results.append(
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  {
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  self.id_column: cmpd_id,
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  self.target: cmpd_target,
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+ "nn_target": row["nn_target"],
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+ "nn_target_diff": row["nn_target_diff"],
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+ "nn_distance": row["nn_distance"],
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+ "gradient": row["gradient"], # Keep Phase 1 gradient
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  "neighbor_median": neighbor_median,
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  "neighbor_median_diff": median_diff,
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- "mean_distance": mean_distance,
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- "gradient": median_diff / (mean_distance + epsilon),
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  }
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  )
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@@ -19,7 +19,7 @@ from typing import List, Tuple, Optional, Dict
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  # Template Placeholders
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  TEMPLATE_PARAMS = {
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  "target": "udm_asy_res_efflux_ratio",
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- "features": ['chi2v', 'fr_sulfone', 'chi1v', 'bcut2d_logplow', 'fr_piperzine', 'kappa3', 'smr_vsa1', 'slogp_vsa5', 'fr_ketone_topliss', 'fr_sulfonamd', 'fr_imine', 'fr_benzene', 'fr_ester', 'chi2n', 'labuteasa', 'peoe_vsa2', 'smr_vsa6', 'bcut2d_chglo', 'fr_sh', 'peoe_vsa1', 'fr_allylic_oxid', 'chi4n', 'fr_ar_oh', 'fr_nh0', 'fr_term_acetylene', 'slogp_vsa7', 'slogp_vsa4', 'estate_vsa1', 'vsa_estate4', 'numbridgeheadatoms', 'numheterocycles', 'fr_ketone', 'fr_morpholine', 'fr_guanido', 'estate_vsa2', 'numheteroatoms', 'fr_nitro_arom_nonortho', 'fr_piperdine', 'nocount', 'numspiroatoms', 'fr_aniline', 'fr_thiophene', 'slogp_vsa10', 'fr_amide', 'slogp_vsa2', 'fr_epoxide', 'vsa_estate7', 'fr_ar_coo', 'fr_imidazole', 'fr_nitrile', 'fr_oxazole', 'numsaturatedrings', 'fr_pyridine', 'fr_hoccn', 'fr_ndealkylation1', 'numaliphaticheterocycles', 'fr_phenol', 'maxpartialcharge', 'vsa_estate5', 'peoe_vsa13', 'minpartialcharge', 'qed', 'fr_al_oh', 'slogp_vsa11', 'chi0n', 'fr_bicyclic', 'peoe_vsa12', 'fpdensitymorgan1', 'fr_oxime', 'molwt', 'fr_dihydropyridine', 'smr_vsa5', 'peoe_vsa5', 'fr_nitro', 'hallkieralpha', 'heavyatommolwt', 'fr_alkyl_halide', 'peoe_vsa8', 'fr_nhpyrrole', 'fr_isocyan', 'bcut2d_chghi', 'fr_lactam', 'peoe_vsa11', 'smr_vsa9', 'tpsa', 'chi4v', 'slogp_vsa1', 'phi', 'bcut2d_logphi', 'avgipc', 'estate_vsa11', 'fr_coo', 'bcut2d_mwhi', 'numunspecifiedatomstereocenters', 'vsa_estate10', 'estate_vsa8', 'numvalenceelectrons', 'fr_nh2', 'fr_lactone', 'vsa_estate1', 'estate_vsa4', 'numatomstereocenters', 'vsa_estate8', 'fr_para_hydroxylation', 'peoe_vsa3', 'fr_thiazole', 'peoe_vsa10', 'fr_ndealkylation2', 'slogp_vsa12', 'peoe_vsa9', 'maxestateindex', 'fr_quatn', 'smr_vsa7', 'minestateindex', 'numaromaticheterocycles', 'numrotatablebonds', 'fr_ar_nh', 'fr_ether', 'exactmolwt', 'fr_phenol_noorthohbond', 'slogp_vsa3', 'fr_ar_n', 'sps', 'fr_c_o_nocoo', 'bertzct', 'peoe_vsa7', 'slogp_vsa8', 'numradicalelectrons', 'molmr', 'fr_tetrazole', 'numsaturatedcarbocycles', 'bcut2d_mrhi', 'kappa1', 'numamidebonds', 'fpdensitymorgan2', 'smr_vsa8', 'chi1n', 'estate_vsa6', 'fr_barbitur', 'fr_diazo', 'kappa2', 'chi0', 'bcut2d_mrlow', 'balabanj', 'peoe_vsa4', 'numhacceptors', 'fr_sulfide', 'chi3n', 'smr_vsa2', 'fr_al_oh_notert', 'fr_benzodiazepine', 'fr_phos_ester', 'fr_aldehyde', 'fr_coo2', 'estate_vsa5', 'fr_prisulfonamd', 'numaromaticcarbocycles', 'fr_unbrch_alkane', 'fr_urea', 'fr_nitroso', 'smr_vsa10', 'fr_c_s', 'smr_vsa3', 'fr_methoxy', 'maxabspartialcharge', 'slogp_vsa9', 'heavyatomcount', 'fr_azide', 'chi3v', 'smr_vsa4', 'mollogp', 'chi0v', 'fr_aryl_methyl', 'fr_nh1', 'fpdensitymorgan3', 'fr_furan', 'fr_hdrzine', 'fr_arn', 'numaromaticrings', 'vsa_estate3', 'fr_azo', 'fr_halogen', 'estate_vsa9', 'fr_hdrzone', 'numhdonors', 'fr_alkyl_carbamate', 'fr_isothiocyan', 'minabspartialcharge', 'fr_al_coo', 'ringcount', 'chi1', 'estate_vsa7', 'fr_nitro_arom', 'vsa_estate9', 'minabsestateindex', 'maxabsestateindex', 'vsa_estate6', 'estate_vsa10', 'estate_vsa3', 'fr_n_o', 'fr_amidine', 'fr_thiocyan', 'fr_phos_acid', 'fr_c_o', 'fr_imide', 'numaliphaticrings', 'peoe_vsa6', 'vsa_estate2', 'nhohcount', 'numsaturatedheterocycles', 'slogp_vsa6', 'peoe_vsa14', 'fractioncsp3', 'bcut2d_mwlow', 'numaliphaticcarbocycles', 'fr_priamide', 'nacid', 'nbase', 'naromatom', 'narombond', 'sz', 'sm', 'sv', 'sse', 'spe', 'sare', 'sp', 'si', 'mz', 'mm', 'mv', 'mse', 'mpe', 'mare', 'mp', 'mi', 'xch_3d', 'xch_4d', 'xch_5d', 'xch_6d', 'xch_7d', 'xch_3dv', 'xch_4dv', 'xch_5dv', 'xch_6dv', 'xch_7dv', 'xc_3d', 'xc_4d', 'xc_5d', 'xc_6d', 'xc_3dv', 'xc_4dv', 'xc_5dv', 'xc_6dv', 'xpc_4d', 'xpc_5d', 'xpc_6d', 'xpc_4dv', 'xpc_5dv', 'xpc_6dv', 'xp_0d', 'xp_1d', 'xp_2d', 'xp_3d', 'xp_4d', 'xp_5d', 'xp_6d', 'xp_7d', 'axp_0d', 'axp_1d', 'axp_2d', 'axp_3d', 'axp_4d', 'axp_5d', 'axp_6d', 'axp_7d', 'xp_0dv', 'xp_1dv', 'xp_2dv', 'xp_3dv', 'xp_4dv', 'xp_5dv', 'xp_6dv', 'xp_7dv', 'axp_0dv', 'axp_1dv', 'axp_2dv', 'axp_3dv', 'axp_4dv', 'axp_5dv', 'axp_6dv', 'axp_7dv', 'c1sp1', 'c2sp1', 'c1sp2', 'c2sp2', 'c3sp2', 'c1sp3', 'c2sp3', 'c3sp3', 'c4sp3', 'hybratio', 'fcsp3', 'num_stereocenters', 'num_unspecified_stereocenters', 'num_defined_stereocenters', 'num_r_centers', 'num_s_centers', 'num_stereobonds', 'num_e_bonds', 'num_z_bonds', 'stereo_complexity', 'frac_defined_stereo', 'tertiary_amine_count', 'type_i_pattern_count', 'type_ii_pattern_count', 'aromatic_interaction_score', 'molecular_axis_length', 'molecular_asymmetry', 'molecular_volume_3d', 'radius_of_gyration', 'asphericity'],
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+ "features": ['smr_vsa4', 'tpsa', 'numhdonors', 'nhohcount', 'peoe_vsa1', 'mollogp', 'peoe_vsa8', 'nitrogen_span', 'smr_vsa3', 'vsa_estate2', 'chi1v', 'molmr', 'estate_vsa4', 'xc_4dv', 'vsa_estate3', 'vsa_estate6', 'qed', 'estate_vsa8', 'chi2v', 'molecular_asymmetry', 'asphericity', 'vsa_estate4', 'minpartialcharge', 'axp_1d', 'num_s_centers', 'charge_centroid_distance', 'xpc_4dv', 'axp_0dv', 'estate_vsa2', 'peoe_vsa3', 'molecular_axis_length', 'mi', 'aromatic_interaction_score', 'vsa_estate8', 'bcut2d_logphi', 'molecular_volume_3d', 'balabanj', 'fr_al_oh', 'minabsestateindex', 'axp_7dv', 'axp_7d', 'bcut2d_chglo', 'vsa_estate9', 'xch_6d', 'kappa3', 'bcut2d_mrlow', 'estate_vsa3', 'c3sp3', 'chi3n', 'type_ii_pattern_count', 'xp_3d', 'bcut2d_logplow', 'fr_nhpyrrole', 'peoe_vsa9', 'slogp_vsa3', 'peoe_vsa2', 'maxabspartialcharge', 'fpdensitymorgan1', 'xch_7d', 'peoe_vsa11', 'axp_3d', 'bcut2d_mwlow', 'maxestateindex', 'minestateindex', 'radius_of_gyration', 'avgipc', 'smr_vsa6', 'vsa_estate7', 'fpdensitymorgan3', 'estate_vsa6', 'xp_7dv', 'xp_6dv', 'chi4n', 'vsa_estate5', 'fr_imidazole', 'xc_3dv', 'slogp_vsa2', 'num_r_centers', 'xch_5dv', 'bcut2d_mrhi', 'xp_4dv', 'xp_6d', 'mm', 'xpc_6d', 'numsaturatedcarbocycles', 'axp_3dv', 'chi3v', 'numvalenceelectrons', 'mare', 'c1sp2', 'smr_vsa9', 'xp_3dv', 'axp_1dv', 'fpdensitymorgan2', 'slogp_vsa5', 'sps', 'xc_3d', 'bertzct', 'estate_vsa10', 'axp_4d', 'smr_vsa1', 'peoe_vsa10', 'hallkieralpha', 'axp_5dv', 'chi0v', 'xch_7dv', 'mv', 'estate_vsa9', 'fr_ketone_topliss', 'estate_vsa5', 'molwt', 'estate_vsa7', 'type_i_pattern_count', 'xp_5d', 'heavyatommolwt', 'smr_vsa10', 'xc_4d', 'estate_vsa1', 'vsa_estate10', 'axp_6dv', 'axp_2d', 'mp', 'xc_5d', 'xch_6dv', 'xp_7d', 'peoe_vsa7', 'axp_0d', 'xp_2dv', 'axp_6d', 'xc_5dv', 'chi4v', 'xch_4dv', 'mz', 'tertiary_amine_count', 'xpc_6dv', 'peoe_vsa13', 'xpc_4d', 'hybratio', 'axp_5d', 'kappa2', 'slogp_vsa6', 'xpc_5dv', 'phi', 'xch_4d', 'smr_vsa5', 'kappa1', 'xp_5dv', 'bcut2d_chghi', 'numrotatablebonds', 'fr_ar_n', 'maxpartialcharge', 'bcut2d_mwhi', 'peoe_vsa4', 'c3sp2', 'smr_vsa7', 'slogp_vsa4', 'fr_nh0', 'xch_5d', 'slogp_vsa1', 'slogp_vsa10', 'axp_2dv', 'xc_6dv', 'numaliphaticrings', 'axp_4dv', 'chi0', 'labuteasa', 'c1sp3', 'numaliphaticcarbocycles', 'xp_0dv', 'fr_hoccn', 'fr_piperdine', 'fractioncsp3', 'si', 'slogp_vsa8', 'sv', 'fr_thiazole', 'fr_guanido', 'spe', 'peoe_vsa6', 'fr_pyridine', 'nocount', 'fr_piperzine', 'chi2n', 'chi0n', 'mse', 'fr_aniline', 'xpc_5d', 'peoe_vsa12', 'fr_ndealkylation1', 'fr_al_oh_notert', 'fr_methoxy', 'numheteroatoms', 'c2sp3', 'fr_nh1', 'sp', 'chi1', 'peoe_vsa14', 'numatomstereocenters', 'ringcount', 'mpe', 'slogp_vsa7', 'frac_defined_stereo', 'fr_morpholine', 'c2sp2', 'xp_2d', 'vsa_estate1', 'slogp_vsa11', 'fr_benzene', 'nbase', 'xp_4d', 'num_stereocenters', 'fr_arn', 'minabspartialcharge', 'chi1n', 'sare', 'numspiroatoms', 'xp_0d', 'fr_aryl_methyl', 'fr_imine', 'fr_priamide', 'num_defined_stereocenters', 'numunspecifiedatomstereocenters', 'fr_oxazole'],
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  "compressed_features": [],
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  "train_all_data": True,
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  "hyperparameters": {},
@@ -312,6 +312,8 @@ def cross_fold_inference(workbench_model: Any, nfolds: int = 5) -> Tuple[pd.Data
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  id_col = fs.id_column
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  target_col = workbench_model.target()
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  feature_cols = workbench_model.features()
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+ print(f"Target column: {target_col}")
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+ print(f"Feature columns: {len(feature_cols)} features")
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  # Convert string[python] to object, then to category for XGBoost compatibility
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  # This avoids XGBoost's issue with pandas 2.x string[python] dtype in categorical categories
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: workbench
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- Version: 0.8.197
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+ Version: 0.8.198
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  Summary: Workbench: A Dashboard and Python API for creating and deploying AWS SageMaker Model Pipelines
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  Author-email: SuperCowPowers LLC <support@supercowpowers.com>
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  License: MIT License
@@ -6,7 +6,7 @@ workbench/algorithms/dataframe/data_source_eda.py,sha256=WgVL6tzBCw1tznQr8RQ6daQ
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  workbench/algorithms/dataframe/feature_space_proximity.py,sha256=6RxzvbpLdDkHMm1D49Nv59SFcyYUj8bisd6_5EpBEGI,3515
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  workbench/algorithms/dataframe/fingerprint_proximity.py,sha256=nGxfmYQ3bfMtvs90s4p7gaY9DN4gijdDU7R6B2lRHgo,5825
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  workbench/algorithms/dataframe/projection_2d.py,sha256=zK4hc0OQrySmfcfFg8y0GxEL34uDNqvZL4OgttB9vRs,7834
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- workbench/algorithms/dataframe/proximity.py,sha256=AkzcXvSEtbJdJwHYWoitaGOrTMUJZbrPzTvY8q-Fr8s,15383
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+ workbench/algorithms/dataframe/proximity.py,sha256=MYVkQfn-pqXCm25dwiXaBDQngtBaN8lM8yeILJAstjY,15468
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  workbench/algorithms/dataframe/storage/aggregation.py,sha256=VuTb7A6Vh6IS5djZeItvOLnnEOlf7tzMQ8OaYIuftvU,2852
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  workbench/algorithms/dataframe/storage/feature_resolution.py,sha256=w_iLf8EFTg7Jc5laH-bsq8MEtZVqcg05W-GihCqR-r4,9450
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  workbench/algorithms/dataframe/storage/feature_spider.py,sha256=uIZ4JHIKuhpy08wBFReSrohb5DGxx8vGroHUbjPm1jE,14353
@@ -123,6 +123,8 @@ workbench/core/views/view.py,sha256=8pZSVDhOFMnAh49ccvnvjQs0dWpiA5IeHaYrztRcqkM,
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  workbench/core/views/view_utils.py,sha256=CwOlpqXpumCr6REi-ey7Qjz5_tpg-s4oWHmlOVu8POQ,12270
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  workbench/core/views/storage/mdq_view.py,sha256=qf_ep1KwaXOIfO930laEwNIiCYP7VNOqjE3VdHfopRE,5195
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  workbench/model_scripts/script_generation.py,sha256=dLxVRrvrrI_HQatJRAXta6UEbFFbkgITNvDJllQZyCM,7905
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+ workbench/model_scripts/__pycache__/script_generation.cpython-312.pyc,sha256=p3q4RDNMkLKpt4UMrdY94rZcZGgvNcTstS2r5ZIvrSg,7570
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+ workbench/model_scripts/__pycache__/script_generation.cpython-313.pyc,sha256=eodln_BQ1mvfLxE6n1_6WFtMBTKqepwWmXubBk7pL1s,7559
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  workbench/model_scripts/custom_models/chem_info/Readme.md,sha256=mH1lxJ4Pb7F5nBnVXaiuxpi8zS_yjUw_LBJepVKXhlA,574
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  workbench/model_scripts/custom_models/chem_info/mol_descriptors.py,sha256=c8gkHZ-8s3HJaW9zN9pnYGK7YVW8Y0xFqQ1G_ysrF2Y,18789
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  workbench/model_scripts/custom_models/chem_info/mol_standardize.py,sha256=qPLCdVMSXMOWN-01O1isg2zq7eQyFAI0SNatHkRq1uw,17524
@@ -133,7 +135,7 @@ workbench/model_scripts/custom_models/meta_endpoints/example.py,sha256=hzOAuLhIG
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  workbench/model_scripts/custom_models/network_security/Readme.md,sha256=Z2gtiu0hLHvEJ1x-_oFq3qJZcsK81sceBAGAGltpqQ8,222
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+ workbench-0.8.198.dist-info/RECORD,,